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Crystal Structure of Fructose-Bisphosphate Aldolase, Class I from Porphyromonas gingivalis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1.2 M Ammonium citrate tribasic, 100 mM BTP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.09 60.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.737 α = 90 b = 68.737 β = 90 c = 154.113 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD SBC-3 mirrors 2005-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.44 38.89 99.7 0.144 7 8.5 16237 16237
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.53 99.8 0.427 3.8 6.1 1602
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.46 38.89 14343 14343 1612 99.74 0.18686 0.18686 0.18167 0.1768 0.23172 0.2244 RANDOM 35.452
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.51 0.25 0.51 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.854 r_dihedral_angle_4_deg 20.415 r_dihedral_angle_3_deg 18.104 r_dihedral_angle_1_deg 6.022 r_scangle_it 3.8 r_scbond_it 2.352 r_angle_refined_deg 1.517 r_mcangle_it 1.24 r_mcbond_it 0.806 r_symmetry_hbond_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.854 r_dihedral_angle_4_deg 20.415 r_dihedral_angle_3_deg 18.104 r_dihedral_angle_1_deg 6.022 r_scangle_it 3.8 r_scbond_it 2.352 r_angle_refined_deg 1.517 r_mcangle_it 1.24 r_mcbond_it 0.806 r_symmetry_hbond_refined 0.322 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXCD phasing SHELXD phasing SHELXE model building MLPHARE phasing SOLVE phasing RESOLVE phasing PHENIX phasing